The chimney we have is original Victorian, with clay liner. I don't know how good this liner is, other than the fact that it has been in regular use with a 12kW open gas fire since we moved in without any problems. I wondered whether this existing liner could be used (at least partially) - it's not as if the chimney isn't lined, but...

If we got it cleaned and smoke tested, and it passed, would it be possible to partially re-line with flexible liner, say 2m worth from the top of the insert and part way up the chimney? Would this work? Because the chimney is tall, there's no real way I could line it myself, and so if it needs to be lined to accommodate a wood burner then I might have to lean toward a gas insert instead, which would be a shame...

If the stove your picking out is 6" then you should be fine, 5" (or approx metric) would be cutting it close. You actually will probably overdraft on a 8" 40' tall chimney. Gas might be the way to go. Thats alot of chimney !!